My guess from what we've seen so for would be that one (MC?) couldn't kill the child while the other (Sonja?) followed orders and went through with it.
The other thing is that it seems a bit amateurish to not tell them who the target is going to be. But maybe the mission was different in the beginning. But there we had another human with powers and Meredith was involved and/or knew about it.
And the final animations this update really are great. Not just the Gloria one. The whole "moving out" of all the involved parties was awesome as well. The APC designs reminds me of the Aliens movie/games.